Thanks for distributing/supporting NODDI so nicely. I wonder if you could tell me how the noise floor is handled by the NODDI Matlab toolbox.
In particular, is it included in the model? I notice this in the text of your 2012 paper:
"The procedure determines the maximum likelihood estimates of the parameters, using a Rician noise model, with the Gauss-Newton nonlinear optimization technique.
The starting point for the nonlinear optimization is obtained from an initial brute-force search over a coarse and regular grid of physically plausible settings."
and I notice in your matlab fitting code a GridSearch algorithm with a Rician distribution, but I am failing to connect the two conceptually to know how the noise floor is/isn't modeled when I use this implementation on my own data (which is ex-vivo modeling).
Thanks much far any insight on this.